From 5505ba8bf177f292906e3655a44270dde4a70342 Mon Sep 17 00:00:00 2001 From: jdavis3141 Date: Tue, 15 Oct 2024 11:36:02 -0400 Subject: [PATCH] Try separator in groovy --- scripts/make_config_file.groovy | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/make_config_file.groovy b/scripts/make_config_file.groovy index 2cf6ad7f..9dfb916d 100644 --- a/scripts/make_config_file.groovy +++ b/scripts/make_config_file.groovy @@ -28,14 +28,14 @@ pipeline { booleanParam(name: 'COLLAPSE', defaultValue: true, description: 'Collapse replicates.') booleanParam(name: 'REMOVE_DATA', defaultValue: false, description: 'Select if there is experimental data that needs to be removed prior to normalization.') booleanParam(name: 'CONVERT_SUSHI', defaultValue: false, description: 'Convert output column headers to format for MTS pipeline and upload to s3.') - booleanParam(name: 'RUN_EPS_QC', defaultValue: false, description: 'Run EPS QC') - string(name: 'BUILD_DIR', defaultValue: '/cmap/obelix/pod/prismSeq/', description: 'Output path to deposit build. Format should be /directory/PROJECT_CODE/BUILD_NAME') + string(name: 'DAYS', defaultValue: '', description: 'If running the sushi_to_mts module, provide any days/timepoints (separated by commas) that should be dropped from output data. No quotes needed (ie, 2,8).') + booleanParam(name: 'RUN_EPS_QC', defaultValue: false, description: 'Generates an EPS specific QC report.') + string(name: 'BUILD_DIR', defaultValue: '/cmap/obelix/pod/prismSeq/', description: 'Output path to deposit build files. Format should be /directory/PROJECT_CODE/BUILD_NAME') string(name: 'BUILD_NAME', defaultValue: '', description: 'Build name, files will start with this prefix.') string(name: 'SEQ_TYPE', defaultValue: 'DRAGEN', description: 'Choose DRAGEN, MiSeq, HiSeq, or NovaSeq. MiSeq and HiSeq/NovaSeq return files named differently. This setting sets the INDEX_1, INDEX_2, and BARCODE_SUFFIX parameters in fastq2readcount. Select DRAGEN if fastq files are from the DRAGEN pipeline from GP. Choosing NovaSeq reverses index 2.') - string(name: 'CTL_TYPES', defaultValue: 'negcon', description: 'Type to mark as control in compute_LFC') - string(name: 'SIG_COLS', defaultValue: 'cell_set,treatment,dose,dose_unit,day', description: 'Columns that ecode all experimental conditions') + string(name: 'SIG_COLS', defaultValue: 'cell_set,treatment,dose,dose_unit,day', description: 'Columns that encode all experimental conditions') + string(name: 'CTL_TYPES', defaultValue: 'negcon', description: 'Perturbation type to mark as negative control when computing fold changes.') string(name: 'CONTROL_COLS', defaultValue: 'cell_set,day', description: 'Set of columns that define individual controls; should be a subset of SIG_COLS') - string(name: 'DAYS', defaultValue: '', description: 'If running the sushi_to_mts module, provide any days/timepoints (separated by commas) that should be dropped from output data. No quotes needed (ie, 2,8).') separator( name: "Group_1", sectionHeader: "Do Not Edit",